The following allowed me to eliminate the duplicated commits in one step
via git merge --squash and then successfully push back to the bioc-git
server. After this I was able to switch to the swap branch approach to
avoid similar problems in the future.
Example here for master branch:
git checkout master
git pull upstream master # just in case
git reset --hard <commit_id> # Reset the current branch to the commit
right before dups started
git merge --squash HEAD@{1} # Squashes duplicated commits from chosen
<commit_id> to HEAD@{1} (state right before previous reset step)
git commit -am "some_message" # Commit squashed changes
git push upstream master # Push to bioc-git server
I am not sure if the above is the best solution but I thought I report it
here in case others experience similar problems. BTW: in my case the
duplicates were all generated in the upstream merge (step 6) of the
instructions here: https://goo.gl/wWVEeT. None of the parent branches (on
github or bioc) used in this merge step contained duplicated commits at
least as far as I have checked so far. Perhaps some of this relates back to
the git svn/rebase steps we used under the old git mirror?
Just in case, the following command is very helpful to identify duplicate
commits based on patch-id. Commits with identical patch-ids are very likely
to have identical content.
git rev-list master | xargs -r -L1 git diff-tree -m -p | git patch-id
| sort | uniq -w40 -D | cut -c42-80 | xargs -r git log --no-walk
--pretty=format:"%h %ad %an (%cn) %s" --date-order --date=iso
After duplicated commit pairs have been identified, one can check with diff
or vimdiff whether their content is identical:
git --no-pager show <commit_id1> > zzz1
git --no-pager show <commit_id2> > zzz2
vimdiff zzz1 zzz2
Thomas
On Fri, Sep 8, 2017 at 9:16 PM Thomas Girke <thomas.gi...@ucr.edu> wrote:
Since our duplicate commits slipped through to Bioc (probably during
> pre-receive hook downtime), the only option I see, to actually get to the
> actual swap branch step, is to first fix the current duplicate problem in
> the upstream Bioc remote by resetting the affected branches back to the
> commit right before the duplicates occurred. Manual fixes seem unrealistic
> given the number of instances. However, when following (see below) the
> reset instructions here (https://goo.gl/SeNCPk) I am getting a “hook
> declined” error. Not sure how to get beyond this? Or are there alternative
> solutions I should try?
>
> Interestingly, according to the instructions on the top of the Bioc
> instructions of this very topic (https://goo.gl/SeNCPk) I am supposedly
> now someone who "went nuclear". Wasn't this term introduced (or perhaps
> just abused) by the last presidential campaign? How can it get anymore
> frustrating than being affiliated with this outcome :).
>
> Thomas
>
> git reset --hard e3a8d2122a65305c478276e538faace277ea9ed6
> git push -f origin master
> git push -f upstream master
>
> Total 0 (delta 0), reused 0 (delta 0)
> remote: FATAL: + refs/heads/master packages/ChemmineR t.girke DENIED by
> fallthru
> remote: error: hook declined to update refs/heads/master
> To g...@git.bioconductor.org:packages/ChemmineR.git
> ! [remote rejected] master -> master (hook declined)
> error: failed to push some refs to
> 'g...@git.bioconductor.org:packages/ChemmineR.git'
>
>
>
> On Fri, Sep 8, 2017 at 12:21 PM Turaga, Nitesh <
> nitesh.tur...@roswellpark.org> wrote:
>
>> Hi Thomas,
>>
>> Thanks for understanding. Swapping branches is the best solution I could
>> come up with, and would advice you to go ahead with that.
>>
>> The catching of false positives was a couple of bugs in our pre-receive
>> hooks code, which we have since fixed. I’m glad to have made the shift to
>> Git, and hope the community enjoys it.
>>
>> Best Regards,
>>
>> Nitesh
>>
>>
>> > On Sep 8, 2017, at 2:59 PM, Thomas Girke <thomas.gi...@ucr.edu> wrote:
>> >
>> > Dear Martin and Nitesh,
>> >
>> > If swapping branches is the recommended solution then I will do so. The
>> on/off situation with the duplicate commit error misled me to believe it is
>> a temporary problem on the Bioc end. I am sorry for the extra noise my
>> message may have caused.
>> >
>> > As a group that maintains GitHub versions of all our Bioc packages, we
>> are extremely excited about the recent git transition. Thanks Nitesh (and
>> your colleagues) for doing all of this. It must have been a massive effort
>> for so many packages.
>> >
>> > Best,
>> >
>> > Thomas
>> >
>> >
>> > On Fri, Sep 8, 2017 at 7:11 AM Martin Morgan <
>> martin.mor...@roswellpark.org> wrote:
>> > On 09/08/2017 09:34 AM, Turaga, Nitesh wrote:
>> > > Hi Thomas,
>> > >
>> > > So, you do actually have a “duplicate” commit and you should NOT be
>> pushing this to the bioc-git server. Notice that the body of both those
>> commits is the same.
>> > >
>> > > If you want to check the rest of your commit history, please try `git
>> log - -oneline` . And you will see that you will have multiple duplicate
>> commits. This compromises your commit history on both your Github repo, and
>> on the bioc-git server.
>> > >
>> > > As suggested in the error message,
>> > >
>> > > remote: Take a look at the documentation to fix this,
>> > > remote:
>> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
>> ,
>> > > particularly, point #8 (force Bioconductor master to
>> Github master).
>> > >
>> > > I would advice you to take a look at that. If you have other thoughts
>> on how to solve this problem, I’d be happy to listen.
>> >
>> > Seemed like Thomas wasn't eager to replace his current master with
>> > git.bicoonductor.org's master (swap branches). Maybe one thing that
>> > makes it more palatable is that the current master can be retained,
>> > e.g., as a branch master_archive.
>> >
>> > What are the alternatives to forcing master branch to be
>> > git.bioconductor.org's version?
>> >
>> > Selectively removing duplicate commits (how does one do that?)
>> >
>> > Cherry-picking (into the official Bioconductor branch) rather than
>> merging?
>> >
>> > I know it'll get hairy here, and maybe no easy or complete or simple
>> > solution... maybe seeing the steps required for alternative solutions
>> > would make the branch swap solution more palatable :)
>> >
>> > Martin
>> >
>> > >
>> > > Best,
>> > >
>> > > Nitesh
>> > >
>> > >
>> > >
>> > >> On Sep 7, 2017, at 11:02 PM, Thomas Girke <thomas.gi...@ucr.edu>
>> wrote:
>> > >>
>> > >> Sure, it’s pretty long but here it is:
>> > >>
>> > >> git show 8210e1e04e8dc6819b84820077293d8d61914cf5
>> > >> commit 8210e1e04e8dc6819b84820077293d8d61914cf5
>> > >> Author: Kevin Horan <
>> > >> kho...@cs.ucr.edu
>> > >>>
>> > >> Date: Fri Jun
>> > >> 30 21:37:15 2017 +0000
>> > >>
>> > >>
>> > >> fix
>> > >> for RSQLite 2
>> > >>
>> > >>
>> > >> git-svn-id: file:///home/git/
>> > >>
>> hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ChemmineR@130824
>> bc3139a8-67e5-0310
>> > >> -9ffc-ced21a209358
>> > >>
>> > >> diff --git a/DESCRIPTION b/DESCRIPTION
>> > >> index 4b4d514..c96da6e
>> > >> 100644
>> > >>
>> > >> --- a/DESCRIPTION
>> > >> +++ b/DESCRIPTION
>> > >> @@ -
>> > >> 1,8 +1,8
>> > >> @@
>> > >> Package: ChemmineR
>> > >> Type: Package
>> > >> Title: Cheminformatics Toolkit
>> > >> for
>> > >> R
>> > >> -Version:
>> > >> 2.28.0
>> > >>
>> > >> -Date:
>> > >> 2016-11-30
>> > >>
>> > >> +Version:
>> > >> 2.28.1
>> > >>
>> > >> +Date:
>> > >> 2017-6-30
>> > >>
>> > >> Author: Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke
>> > >> Maintainer: Thomas Girke <
>> > >> thomas.gi...@ucr.edu
>> > >>>
>> > >> Description: ChemmineR is a cheminformatics package
>> > >> for analyzing drug-like small molecule data in R. Its latest version
>> contains functions for
>> > >> efficient processing of large numbers of molecules, physicochemical
>> > >> diff --git a/R/compound_db.R b/R/compound_db.R
>> > >> index 76d1f6c..970c4a2
>> > >> 100644
>> > >>
>> > >> --- a/R/compound_db.R
>> > >> +++ b/R/compound_db.R
>> > >> @@ -
>> > >> 38,7 +38,7 @@ initDb <- function
>> > >> (handle){
>> > >> collapse=
>> > >> ""),";",fixed=TRUE
>> > >> ))
>> > >>
>> > >> #print(statements)
>> > >>
>> > >>
>> > >> - Map(
>> > >> function
>> > >> (sql) dbOp(dbGetQuery(conn,sql)),statements)
>> > >> + Map(
>> > >> function
>> > >> (sql) dbOp(dbExecute(conn,sql)),statements)
>> > >> }
>> > >> conn
>> > >> }
>> > >> @@ -
>> > >> 54,7 +54,7 @@ dbTransaction <- function
>> > >> (conn,expr){
>> > >>
>> > >> # be paranoid about setting this as bad things will happen if its
>> not set
>> > >>
>> > >> enableForeignKeys(conn)
>> > >>
>> > >> - dbGetQuery(conn,
>> > >> "BEGIN TRANSACTION"
>> > >> )
>> > >> + dbExecute(conn,
>> > >> "BEGIN TRANSACTION"
>> > >> )
>> > >> ret=expr
>> > >> dbCommit(conn)
>> > >> ret
>> > >> @@ -
>> > >> 64,8 +64,11 @@ dbTransaction <- function
>> > >> (conn,expr){
>> > >>
>> > >> stop(paste("db error inside transaction: "
>> > >> ,e$message))
>> > >> })
>> > >> }
>> > >>
>> > >> -dbGetQueryChecked <-
>> > >> function(conn,statement,...
>> > >> ){
>> > >> - ret=dbGetQuery(conn,statement)
>> > >> +dbGetQueryChecked <-
>> > >> function(conn,statement,execute=FALSE,...
>> > >> ){
>> > >> +
>> > >> if(execute == TRUE
>> > >> )
>> > >> + ret=dbExecute(conn,statement)
>> > >> +
>> > >> else
>> > >>
>> > >>
>> > >> + ret=dbGetQuery(conn,statement)
>> > >> err=dbGetException(conn)
>> > >>
>> > >> if(err$errorMsg[1] != "OK"
>> > >> )
>> > >>
>> > >> stop("error in dbGetQuery: ",err$errorMsg," "
>> > >> ,traceback())
>> > >> @@ -
>> > >> 895,10 +898,10 @@ createFeature <- function
>> > >> (conn,name, isNumeric){
>> > >> dbGetQueryChecked(conn,
>> > >> paste(
>> > >> "CREATE TABLE feature_",name,
>> > >> " (
>> > >> compound_id INTEGER PRIMARY KEY REFERENCES
>> compounds(compound_id) ON DELETE CASCADE ON UPDATE CASCADE, "
>> > >> ,
>> > >> -
>> > >> "",name," ",sqlType," )",sep=""
>> > >> ))
>> > >> +
>> > >> "",name," ",sqlType," )",sep=""),execute=TRUE
>> > >> )
>> > >>
>> > >>
>> > >> #print("made table")
>> > >>
>> > >> - dbGetQuery(conn,paste(
>> > >> "CREATE INDEX feature_",name,
>> > >> "_index ON
>> > >> + dbExecute(conn,paste("
>> > >> CREATE INDEX feature_",name,"
>> > >> _index ON
>> > >>
>> feature_
>> > >> ",name,"(\"",name,"\")",sep=""
>> > >> ))
>> > >>
>> > >> #print("made index")
>> > >>
>> > >>
>> > >> @@ -
>> > >> 913,7 +916,7 @@ insertDef <- function
>> > >> (conn,data) {
>> > >>
>> > >> "VALUES(:definition,:definition_checksum,:format)",sep=""
>> > >> ), bind.data=data[fields])
>> > >> }
>> > >> else if(inherits(conn,"PostgreSQLConnection"
>> > >> )){
>> > >>
>> > >> if(debug) print(data[,"definition_checksum"
>> > >> ])
>> > >> - apply(data[,fields],
>> > >> 1,function
>> > >> (row) dbOp(dbGetQuery(conn,
>> > >> + apply(data[,fields],
>> > >> 1,function
>> > >> (row) dbOp(dbExecute(conn,
>> > >>
>> > >> "INSERT INTO compounds(definition,definition_checksum,format)
>> VALUES($1,$2,$3)"
>> > >> ,
>> > >> row)))
>> > >> }
>> > >> else
>> > >> {
>> > >> @@ -
>> > >> 990,7 +993,7 @@ insertDescriptor <- function
>> > >> (conn,data){
>> > >> })
>> > >> apply(data[,fields2],
>> > >> 1,function
>> > >> (row) {
>> > >> row[
>> > >> 2] = descTypes[row[2]] #translate descriptor_type to
>> descriptor_type_id
>> > >>
>> > >> - dbTransaction(conn,dbGetQuery(conn, paste(
>> > >> "INSERT INTO compound_descriptors(compound_id,
>> > >> + dbTransaction(conn,dbExecute(conn, paste("
>> > >> INSERT INTO compound_descriptors(compound_id,
>> > >>
>> descriptor_id)
>> > >> ",
>> > >> "
>> > >> VALUES( (SELECT compound_id FROM compounds WHERE definition_checksum
>> = $1
>> > >> ),
>> > >>
>> (SELECT descriptor_id FROM descriptors
>> > >> @@ -
>> > >> 1006,7 +1009,7 @@ insertDescriptorType <- function
>> > >> (conn,data){
>> > >>
>> bind.data=data)
>> > >> }
>> > >> else if(inherits(conn,"PostgreSQLConnection"
>> > >> )){
>> > >> apply(data,
>> > >> 1,function
>> > >> (row)
>> > >> - dbGetQuery(conn,paste(
>> > >> "INSERT INTO descriptor_types(descriptor_type) VALUES($1)"
>> > >> ),row))
>> > >> + dbExecute(conn,paste(
>> > >> "INSERT INTO descriptor_types(descriptor_type) VALUES($1)"
>> > >> ),row))
>> > >> }
>> > >> else
>> > >> {
>> > >>
>> > >> stop("database ",class(conn)," unsupported"
>> > >> )
>> > >> }
>> > >> @@ -
>> > >> 1019,7 +1022,7 @@ updatePriorities <- function
>> > >> (conn,data){
>> > >>
>> descriptor_id=:descriptor_id
>> > >> ", bind.data=data)
>> > >> }else if(inherits(conn,"
>> > >> PostgreSQLConnection
>> > >> ")){
>> > >> apply(data[,c("
>> > >> compound_id","descriptor_id","priority
>> > >> ")],1,function(row)
>> > >> - dbGetQuery(conn,paste("
>> > >> UPDATE compound_descriptors SET priority = $3 WHERE compound_id=$1
>> > >> AND
>> > >> + dbExecute(conn,paste(
>> > >> "UPDATE compound_descriptors SET priority = $3 WHERE compound_id=$1
>> AND
>> > >>
>> descriptor_id=$2"
>> > >> ),row))
>> > >> }
>> > >> else
>> > >> {
>> > >>
>> > >>
>> > >> stop("database ",class(conn)," unsupported"
>> > >> )
>> > >> @@ -
>> > >> 1036,13 +1039,12 @@ getPreparedQuery <- function
>> > >> (conn,statement,bind.data){
>> > >>
>> > >> #dbSendPreparedQuery(conn,statement,bind.data)
>> > >>
>> > >>
>> > >>
>> > >> #print("sending query")
>> > >>
>> > >> - res <- dbSendQuery(conn,statement)
>> > >> + res <- dbSendStatement(conn,statement)
>> > >>
>> > >> #print("after sendQuery")
>> > >>
>> > >> on.exit(dbClearResult(res))
>> > >> #clear result set when this function exits
>> > >>
>> > >>
>> > >> #print("after exit callback registered")
>> > >>
>> > >> - dbBind(res,bind.data)
>> > >> + suppressWarnings(dbBind(res,bind.data))
>> > >>
>> > >> #print("after dbBind")
>> > >>
>> > >> - dbFetch(res)
>> > >> }
>> > >>
>> > >> git show f514d35b793e1d9462b899bf3c76cc06ab4dcc91
>> > >> commit f514d35b793e1d9462b899bf3c76cc06ab4dcc91
>> > >> Author: Kevin Horan <
>> > >> kho...@cs.ucr.edu
>> > >>>
>> > >> Date: Fri Jun
>> > >> 30 21:37:15 2017 +0000
>> > >>
>> > >>
>> > >> fix
>> > >> for RSQLite 2
>> > >>
>> > >>
>> > >> git-svn-id: file:///home/git/
>> > >>
>> hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ChemmineR@130824
>> bc3139a8-67e5-0310
>> > >> -9ffc-ced21a209358
>> > >>
>> > >> diff --git a/DESCRIPTION b/DESCRIPTION
>> > >> index 4b4d514..c96da6e
>> > >> 100644
>> > >>
>> > >> --- a/DESCRIPTION
>> > >> +++ b/DESCRIPTION
>> > >> @@ -
>> > >> 1,8 +1,8
>> > >> @@
>> > >> Package: ChemmineR
>> > >> Type: Package
>> > >> Title: Cheminformatics Toolkit
>> > >> for
>> > >> R
>> > >> -Version:
>> > >> 2.28.0
>> > >>
>> > >> -Date:
>> > >> 2016-11-30
>> > >>
>> > >> +Version:
>> > >> 2.28.1
>> > >>
>> > >> +Date:
>> > >> 2017-6-30
>> > >>
>> > >> Author: Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke
>> > >> Maintainer: Thomas Girke <
>> > >> thomas.gi...@ucr.edu
>> > >>>
>> > >> Description: ChemmineR is a cheminformatics package
>> > >> for analyzing drug-like small molecule data in R. Its latest version
>> contains functions for
>> > >> efficient processing of large numbers of molecules, physicochemical
>> > >> diff --git a/R/compound_db.R b/R/compound_db.R
>> > >> index 76d1f6c..970c4a2
>> > >> 100644
>> > >>
>> > >> --- a/R/compound_db.R
>> > >> +++ b/R/compound_db.R
>> > >> @@ -
>> > >> 38,7 +38,7 @@ initDb <- function
>> > >> (handle){
>> > >> collapse=
>> > >> ""),";",fixed=TRUE
>> > >> ))
>> > >>
>> > >> #print(statements)
>> > >>
>> > >>
>> > >> - Map(
>> > >> function
>> > >> (sql) dbOp(dbGetQuery(conn,sql)),statements)
>> > >> + Map(
>> > >> function
>> > >> (sql) dbOp(dbExecute(conn,sql)),statements)
>> > >> }
>> > >> conn
>> > >> }
>> > >> @@ -
>> > >> 54,7 +54,7 @@ dbTransaction <- function
>> > >> (conn,expr){
>> > >>
>> > >> # be paranoid about setting this as bad things will happen if its
>> not set
>> > >>
>> > >> enableForeignKeys(conn)
>> > >>
>> > >> - dbGetQuery(conn,
>> > >> "BEGIN TRANSACTION"
>> > >> )
>> > >> + dbExecute(conn,
>> > >> "BEGIN TRANSACTION"
>> > >> )
>> > >> ret=expr
>> > >> dbCommit(conn)
>> > >> ret
>> > >> @@ -
>> > >> 64,8 +64,11 @@ dbTransaction <- function
>> > >> (conn,expr){
>> > >>
>> > >> stop(paste("db error inside transaction: "
>> > >> ,e$message))
>> > >> })
>> > >> }
>> > >> -dbGetQueryChecked <-
>> > >> function(conn,statement,...
>> > >> ){
>> > >> - ret=dbGetQuery(conn,statement)
>> > >> +dbGetQueryChecked <-
>> > >> function(conn,statement,execute=FALSE,...
>> > >> ){
>> > >> +
>> > >> if(execute == TRUE
>> > >> )
>> > >> + ret=dbExecute(conn,statement)
>> > >> +
>> > >> else
>> > >>
>> > >>
>> > >> + ret=dbGetQuery(conn,statement)
>> > >> err=dbGetException(conn)
>> > >>
>> > >> if(err$errorMsg[1] != "OK"
>> > >> )
>> > >>
>> > >> stop("error in dbGetQuery: ",err$errorMsg," "
>> > >> ,traceback())
>> > >> @@ -
>> > >> 895,10 +898,10 @@ createFeature <- function
>> > >> (conn,name, isNumeric){
>> > >> dbGetQueryChecked(conn,
>> > >> paste(
>> > >> "CREATE TABLE feature_",name,
>> > >> " (
>> > >> compound_id INTEGER PRIMARY KEY REFERENCES
>> compounds(compound_id) ON DELETE CASCADE ON UPDATE CASCADE, "
>> > >> ,
>> > >> -
>> > >> "",name," ",sqlType," )",sep=""
>> > >> ))
>> > >> +
>> > >> "",name," ",sqlType," )",sep=""),execute=TRUE
>> > >> )
>> > >>
>> > >>
>> > >> #print("made table")
>> > >>
>> > >> - dbGetQuery(conn,paste(
>> > >> "CREATE INDEX feature_",name,
>> > >> "_index ON
>> > >> + dbExecute(conn,paste("
>> > >> CREATE INDEX feature_",name,"
>> > >> _index ON
>> > >>
>> feature_
>> > >> ",name,"(\"",name,"\")",sep=""
>> > >> ))
>> > >>
>> > >> #print("made index")
>> > >>
>> > >>
>> > >> @@ -
>> > >> 913,7 +916,7 @@ insertDef <- function
>> > >> (conn,data) {
>> > >>
>> > >> "VALUES(:definition,:definition_checksum,:format)",sep=""
>> > >> ), bind.data=data[fields])
>> > >> }
>> > >> else if(inherits(conn,"PostgreSQLConnection"
>> > >> )){
>> > >>
>> > >> if(debug) print(data[,"definition_checksum"
>> > >> ])
>> > >> - apply(data[,fields],
>> > >> 1,function
>> > >> (row) dbOp(dbGetQuery(conn,
>> > >> + apply(data[,fields],
>> > >> 1,function
>> > >> (row) dbOp(dbExecute(conn,
>> > >>
>> > >> "INSERT INTO compounds(definition,definition_checksum,format)
>> VALUES($1,$2,$3)"
>> > >> ,
>> > >> row)))
>> > >> }
>> > >> else
>> > >> {
>> > >> @@ -
>> > >> 990,7 +993,7 @@ insertDescriptor <- function
>> > >> (conn,data){
>> > >> })
>> > >> apply(data[,fields2],
>> > >> 1,function
>> > >> (row) {
>> > >> row[
>> > >> 2] = descTypes[row[2]] #translate descriptor_type to
>> descriptor_type_id
>> > >>
>> > >> - dbTransaction(conn,dbGetQuery(conn, paste(
>> > >> "INSERT INTO compound_descriptors(compound_id,
>> > >> + dbTransaction(conn,dbExecute(conn, paste("
>> > >> INSERT INTO compound_descriptors(compound_id,
>> > >>
>> descriptor_id)
>> > >> ",
>> > >> "
>> > >> VALUES( (SELECT compound_id FROM compounds WHERE definition_checksum
>> = $1
>> > >> ),
>> > >>
>> (SELECT descriptor_id FROM descriptors
>> > >> @@ -
>> > >> 1006,7 +1009,7 @@ insertDescriptorType <- function
>> > >> (conn,data){
>> > >>
>> bind.data=data)
>> > >> }
>> > >> else if(inherits(conn,"PostgreSQLConnection"
>> > >> )){
>> > >> apply(data,
>> > >> 1,function
>> > >> (row)
>> > >> - dbGetQuery(conn,paste(
>> > >> "INSERT INTO descriptor_types(descriptor_type) VALUES($1)"
>> > >> ),row))
>> > >> + dbExecute(conn,paste(
>> > >> "INSERT INTO descriptor_types(descriptor_type) VALUES($1)"
>> > >> ),row))
>> > >> }
>> > >> else
>> > >> {
>> > >>
>> > >> stop("database ",class(conn)," unsupported"
>> > >> )
>> > >> }
>> > >> @@ -
>> > >> 1019,7 +1022,7 @@ updatePriorities <- function
>> > >> (conn,data){
>> > >>
>> descriptor_id=:descriptor_id
>> > >> ", bind.data=data)
>> > >> }else if(inherits(conn,"
>> > >> PostgreSQLConnection
>> > >> ")){
>> > >> apply(data[,c("
>> > >> compound_id","descriptor_id","priority
>> > >> ")],1,function(row)
>> > >> - dbGetQuery(conn,paste("
>> > >> UPDATE compound_descriptors SET priority = $3 WHERE compound_id=$1
>> > >> AND
>> > >> + dbExecute(conn,paste(
>> > >> "UPDATE compound_descriptors SET priority = $3 WHERE compound_id=$1
>> AND
>> > >>
>> descriptor_id=$2"
>> > >> ),row))
>> > >> }
>> > >> else
>> > >> {
>> > >>
>> > >> stop("database ",class(conn)," unsupported"
>> > >> )
>> > >> @@ -
>> > >> 1036,13 +1039,12 @@ getPreparedQuery <- function
>> > >> (conn,statement,bind.data){
>> > >>
>> > >>
>> > >> #dbSendPreparedQuery(conn,statement,bind.data)
>> > >>
>> > >>
>> > >>
>> > >> #print("sending query")
>> > >>
>> > >> - res <- dbSendQuery(conn,statement)
>> > >> + res <- dbSendStatement(conn,statement)
>> > >>
>> > >> #print("after sendQuery")
>> > >>
>> > >> on.exit(dbClearResult(res))
>> > >> #clear result set when this function exits
>> > >>
>> > >>
>> > >> #print("after exit callback registered")
>> > >>
>> > >> - dbBind(res,bind.data)
>> > >> + suppressWarnings(dbBind(res,bind.data))
>> > >>
>> > >> #print("after dbBind")
>> > >>
>> > >> - dbFetch(res)
>> > >> }
>> > >>
>> > >> Thomas
>> > >>
>> > >>
>> > >> On Thu, Sep 7, 2017 at 7:39 PM Turaga, Nitesh <
>> nitesh.tur...@roswellpark.org> wrote:
>> > >> Dear Thomas,
>> > >>
>> > >> Can you please send me the output of the two `git show` commands?
>> > >>
>> > >>> git show 8210e1e04e8dc6819b84820077293d8d61914cf5
>> > >>> git show f514d35b793e1d9462b899bf3c76cc06ab4dcc91
>> > >>
>> > >>
>> > >> I’ll need to take a look at those to advice accordingly.
>> > >>
>> > >>
>> > >> Best,
>> > >>
>> > >> Nitesh
>> > >>
>> > >>
>> > >>> On Sep 7, 2017, at 7:04 PM, Thomas Girke <thomas.gi...@ucr.edu>
>> wrote:
>> > >>>
>> > >>> Dear Nitesh,
>> > >>>
>> > >>> In the release branch of our ChemmineR package I am getting a
>> duplicate commit error. Last week we had a similar error across several of
>> our packages but then you made some changes in response to a similar
>> problem reported on the bioc-developer site which eliminated the problem by
>> itself. Now the problem is back again and it is not clear to me how to
>> resolve it. The suggestions given here https://goo.gl/5mk8vV sound a bit
>> harsh.
>> > >>>
>> > >>> tgirke@tgirke-XPS-13-9343
>> > >>> :~/Dropbox/Software/ChemmineR/ChemmineR$ git push upstream
>> RELEASE_3_5
>> > >>> Counting objects:
>> > >>> 26
>> > >>> , done.
>> > >>> Delta compression using up to
>> > >>> 4
>> > >>> threads.
>> > >>> Compressing objects:
>> > >>> 100% (4/4
>> > >>> ), done.
>> > >>> Writing objects:
>> > >>> 100% (4/4), 387 bytes | 0
>> > >>> bytes/s, done.
>> > >>> Total
>> > >>> 4 (delta 3), reused 0 (delta 0
>> > >>> )
>> > >>> remote: Error: duplicate commits.
>> > >>> remote:
>> > >>> remote: There are duplicate commits
>> > >>> in
>> > >>> your commit history, These cannot be
>> > >>> remote: pushed to the Bioconductor git server. Please make sure
>> that this is
>> > >>> remote: resolved.
>> > >>> remote:
>> > >>> remote: Take a look at the documentation to fix this,
>> > >>> remote:
>> > >>>
>> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
>> > >>> ,
>> > >>> remote: particularly, point
>> > >>> #8 (force Bioconductor master to Github master).
>> > >>>
>> > >>> remote:
>> > >>> remote: For more information, or help resolving this issue, contact
>> > >>> remote: <
>> > >>> bioc-devel@r-project.org
>> > >>>> . Provide the error, the package name and
>> > >>> remote: any other details we might need.
>> > >>> remote:
>> > >>> remote: Use
>> > >>> remote:
>> > >>> remote: git show 8210e1e04e8dc6819b84820077293d8d61914cf5
>> > >>> remote: git show f514d35b793e1d9462b899bf3c76cc06ab4dcc91
>> > >>> remote:
>> > >>> remote: to see body of commits.
>> > >>> remote:
>> > >>> To g...@git.bioconductor.org:packages/ChemmineR.git
>> > >>> ! [remote rejected] RELEASE_3_5 -> RELEASE_3_5 (pre-receive hook
>> declined)
>> > >>> error: failed to push some refs to
>> > >>> 'g...@git.bioconductor.org:packages/ChemmineR.git'
>> > >>> Thanks,
>> > >>>
>> > >>> Thomas
>> > >>>
>> > >>> --
>> > >>>
>> > >>> Thomas Girke, Ph.D.
>> > >>>
>> > >>> Professor of Bioinformatics
>> > >>>
>> > >>> Director of HPC Center
>> > >>>
>> > >>> 1207F Genomics Building
>> > >>>
>> > >>> University of California
>> > >>>
>> > >>> Riverside, CA 92521
>> > >>>
>> > >>>
>> > >>>
>> > >>>
>> > >>> E-mail: thomas.gi...@ucr.edu
>> > >>>
>> > >>> Phone/Cell/Text: 951-732-7072 <(951)%20732-7072>
>> > >>
>> > >>
>> > >>
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>> > >
>> > >
>> > >
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>> > > _______________________________________________
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